wwPDB Statement on Retraction of PDB Entries and 2018 ORI Finding

In April 2018, The Office of Research Integrity (ORI) of the U.S. Department of Health and Human Services announced their final Research Misconduct Finding in the case of H.M. Krishna Murthy. It was found that Murthy reported falsified and/or fabricated research in 10 journal publications and 12 corresponding PDB structures. While the ORI was deliberating, 5 Murthy structures in the PDB were obsoleted in accord with wwPDB policies in response to retraction of 4 journal publications (Table 1). In response to a formal request from ORI received on April 13, 2018, the remaining 7 Murthy structures in the PDB were obsoleted, again in accord with wwPDB policies (Table 2).

Typically, authors request that a previously released structure be obsoleted when superseded by a replacement structure resulting from an alternative interpretation of existing data or improved experimental data.

Per wwPDB policy, circumstances occasionally arise under which an obsoleted structure is not superseded by a replacement structure.

  1. The publication is retracted. The associated PDB entry will be obsoleted if requested by the journal. If a request has not been received, the wwPDB will do its best to contact the depositor and co-authors, (former) PIs, journal editors, etc. when made aware of the retraction. If the reason(s) for retraction were such that the associated PDB entry needs to be made obsolete, the wwPDB will obsolete the entry. The citation in the obsoleted entry is the published journal retraction.
  2. The structure is incorrect, and the entry author obsoletes the entry.
  3. A third-party (such as the employer) requests that the entry is obsoleted (e.g., in case of malfeasance). In such cases, the wwPDB will obsolete the entry if either the primary citation for the structure is retracted or a formal report by an appropriate government or supranational agency in the region (e.g., US Office of Research Integrity) is published.

In all cases, the entry must contain a statement specifying the reason for obsoleting the structure.

In December 2009, the University of Alabama at Birmingham (UAB) announced that it planned to retract 12 PDB entries and 10 related publications authored by H.M. Krishna Murthy, in his capacity as Principal Investigator and UAB employee. Following wwPDB review of structures at the request of UAB and in accord with wwPDB policy, 5 of the structures were obsoleted following retraction of the related publications by the journals. Following wwPDB review of structures at the request of UAB and in accord with wwPDB policy, the remaining 7 structures were obsoleted following receipt of the ORI request.

Table 1. PDB entries reviewed at the request of UAB and obsoleted following journal retractions.

PDB ID Date Obsolete Details Citation
1BEF 2009-12-08 The entry is obsoleted due to paper retraction Correction to Murthy et al. (2009) Journal of Biological Chemistry 284, 34468 doi: 10.1074/jbc.A005573200
1CMW 2010-02-09 The entry is obsoleted due to paper retraction Retraction of articles by H. M. Krishna Murthy et al. (2010) Acta Cryst. D66, 222 doi: 10.1107/S0907444910000259
1DF9 2010-02-09 The entry is obsoleted due to paper retraction Retracted: Crystal structure of dengue virus NS3 protease in complex with a Bowman-Birk inhibitor: Implications for flaviviral polyprotein processing and drug design (2000) J. Mol. Biol. 301, 759-767 doi: 10.1006/JMBI.2000.3924
2QID 2010-02-09 The entry is obsoleted due to paper retraction
2HR0 2016-01-13 The entry is obsoleted due to paper retraction Retraction: The structure of complement C3b provides insights into complement activation and regulation Nature 532, 268 (2016); doi: 10.1038/nature16523

Table 2. PDB entries reviewed at the request of UAB and obsoleted following receipt of the ORI request.

PDB ID Date Obsolete Details Citation
1G40 2018-05-09 Entry obsoleted in response to US Office of Research Integrity Notice 2018-07782 Crystal structure of a complement control protein that regulates both pathways of complement activation and binds heparan sulfate proteoglycans (2001) Cell 104, 301-311 doi: 10.1016/S0092-8674(01)00214-8
1G44 2018-05-09 Entry obsoleted in response to US Office of Research Integrity Notice 2018-07782
1L6L 2018-05-09 Entry obsoleted in response to US Office of Research Integrity Notice 2018-07782 Structures of apolipoprotein A-II and a lipid-surrogate complex provide insights into apolipoprotein-lipid interactions (2002) Biochemistry 41, 11681-11691 doi: 10.1021/BI026069W
2OU1 2018-05-09 Entry obsoleted in response to US Office of Research Integrity Notice 2018-07782
1RID 2018-05-09 Entry obsoleted in response to US Office of Research Integrity Notice 2018-07782 Structure of vaccinia complement protein in complex with heparin and potential implications for complement regulation (2004) Proc. Natl. Acad. Sci. USA 101, 8924-8929 doi: 10.1073/PNAS.0400744101
1Y8E 2018-05-09 Entry obsoleted in response to US Office of Research Integrity Notice 2018-07782 Structural basis for antagonism by suramin of heparin binding to vaccinia complement protein (2005) Biochemistry 44, 10757-10765 doi: 10.1021/bi050401x
2A01 2018-05-09 Entry obsoleted in response to US Office of Research Integrity Notice 2018-07782 Crystal structure of human apolipoprotein A-I: Insights into its protective effect against cardiovascular diseases (2006) Proc. Natl. Acad. Sci. USA 103, 2126-2131 doi: 10.1073/pnas.0506877103

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Published: 2018-05-08